Comment lines are allowed at the top of the file. Usually comments
start with a '#' but sometimes with a ';' character. The Biocaml_fasta.fmt
properties allow configuring which is allowed during parsing and
printing.

Description lines begin with the '>' character. Various
conventions are used for the content but there is no
requirement. We simply return the string following the '>'
character.

Sequences are most often a sequence of characters denoting
nucleotides or amino acids, and thus an item's sequence field
is set to a string. Sequences may span multiple lines.

However, sequence lines sometimes are used to provide quality
scores, either as space separated integers or as ASCII encoded
scores. To support the former case, we provide the
Biocaml_fasta.sequence_to_int_list function. For the latter case, see modules
Phred_score and Solexa_score.

FASTA files are used to provide both short sequences and very big
sequences, e.g. a genome. In the latter case, the main API of this
module, which returns each sequence as an in-memory string, might
be too costly. Consider using instead the Biocaml_fasta.read0 function which
does not merge multiple sequence lines into one string. This API
is slightly more difficult to use but perhaps a worthwhile
trade-off.

Some FASTA files include very large sequences on a single
line. This is discouraged and not well supported by this
module. Functions in this module require memory proportional to
the length of a line. Thus, a whole chromosomal sequence on a
single line will consume a large amount of memory. This might not
be a problem given the RAM on most computers.

Format Specifiers:

Variations in the format are controlled by the following settings,
all of which have a default value. These properties are combined
into the Biocaml_fasta.fmt type for convenience and the defaults into
Biocaml_fasta.default_fmt.

allow_empty_lines: Allow lines with only whitespace anywhere in
the file. Default: false.

comments_only_at_top: Allow comments only at the top of the
file. If false, comment lines can occur anywhere but only the ones
at the top are returned. The rest are ignored. Default: true.

max_line_length: Require sequence lines to be shorter than given
length. None means there is no restriction. Note this does not
restrict the length of an item's sequence field because this
can span multiple lines. Default: None.

alphabet: Require sequence characters to be at most those in
given string. None means any character is allowed. Default: None.